Thornton did not feature in the Sunderland first team at the beginning of the 2002–03 season and joined Blackpool on a one month loan in November 2002.[8] He made his debut for Sunderland in a FA Cup third-round replay win over Bolton Wanderers in January 2003, impressing manager Howard Wilkinson who said, "That was the first full game I've seen Sean in and I must say it was a very promising and mature performance. He's certainly a player we want to keep an eye on and bring on but it's now up to him to show he can produce that standard consistently."[9] He made 14 appearances for Sunderland in the 2002–03 season,[10] despite missing part of the season after being called up for the Ireland Under-20 squad for the World Youth Championships in the United Arab Emirates in March 2003.[11] In April 2003, he scored with an impressive volley to give Sunderland an early lead against Chelsea although Sunderland went on to lose the match.[12] He was unable to help Sunderland from being relegated at the end of the season.[13]

Thornton made 13 appearances for Sunderland at the start of the 2003–04 season,[14] before suffering an ankle injury in a reserve team game in October 2003.[15] He returned to the side in January 2004 and made a further 17 appearances,[14] helping Sunderland to the semifinal of the FA Cup,[16] and the Division One playoff semifinal.[17] Thornton was unable to command a regular first team place at the start of the 2004–05 season and by September 2004, was seeking a move away from the club.[18] A transfer did not materialise and with his first team chances limited, he made only 20 appearances for Sunderland in the 2004–05 season.[19] At the end of the season, he was transfer listed.[20]

Following Sunderland's promotion to the Premier League in May 2005,[21] Thornton was sold to Football League One club Doncaster Rovers in July 2005 for a club record fee of £175,000.[22][23] He made 36 appearances for Doncaster in the 2005–06 season,[24] missing several weeks owing to an ankle injury suffered in September 2005 that needed surgery.[25] He helped Doncaster reach the quarterfinals of the Football League Cup, putting in a fine performance and scoring the third goal when Doncaster beat Premier League club, Aston Villa 3–0 in November 2005.[26][27] Manager Dave Penney praised Thornton, saying: "It was a great goal for Sean and he's looking much brighter and sharper these days, and long may that continue."[28] After the game, Thornton said that he felt had made the right move in the summer, saying "It was a gamble for me. I still had two years left on my contract at Sunderland. It was one of them – would I go, would I not go? Obviously we're playing good football and I think I made the right decision. Now, hopefully, we can carry on the success until the end of the season and get promoted. That's the main thing."[29] In the 2006–07 season, Thornton made 41 appearances,[30] and helped Doncaster to victory over Bristol Rovers in the Football League Trophy final in April 2007 when he swung in a corner kick for Graeme Lee to head in to score the extra time winner at the Millennium Stadium, Cardiff.[31]

Thornton was released by Doncaster manager, Sean O'Driscoll at the end of the 2006–07 season,[32] and joined another League One side, Leyton Orient in July 2007 on a two year contract.[33][34] Orient manager Martin Ling said that he was "... pleased to have Sean on board. We've been looking for a creative midfielder and Sean fits the bill perfectly. He will fit into our style of play and I believe we have signed a quality player."[33] He scored on his debut against Southend United in August 2007, with a spectacular free kick from 30 yards in a 2–1 away win,[35] and went on to make 34 appearances in the 2007–08 season,[36] although he missed four matches after being sent off in October 2007 for allegedly punching another player.[37][38] The following season, he joined Shrewsbury Town in September 2008 on a one month loan,[39] where he scored once against Darlington.[40] On his return to Orient, he regained his place in the first team under new manager Geraint Williams and made a total of 34 appearances for Orient in the 2008–09 season in addition to his loan spell at Shrewsbury Town.[41][42] He signed a new one-year contract with Orient in June 2009, with the option of a further year,[42] but was released by Williams' replacement Russell Slade on 9 May 2010 after putting on too much weight.[43]

After false reports that he had signed for FC Metalist Kharkiv,[citation needed] Thornton signed for Aberystwyth Town on a short term contract on 13 September 2011, in a move that was described by the club as 'arguably the biggest signing in Welsh Premier League history'. The midfielder scored his first goal in Aber colours on 11 November 2011, as the Seasiders hammered Port Talbot Town 4-0 at the Genquip Stadium. On 16 November 2011, it was announced that Thornton had agreed to extend his stay with Aberystwyth Town until the end of the 2011/12 Welsh Premier League campaign.[44] He scored his second goal for the club in the 1-1 draw with Afan Lido. He is signed for another season (2012-13) at Aberystwyth Town

After doing pre season with Chris Herbert's men Thornton signed for the ambitious North Wales club on a years pay as you play deal, while he proves his fitness from a ruptured Achilles' tendon. Thornton was influential in Conwy Boroughs undefeated start to the season, also scoring twice in 3 games. But after 6 games in to the 2013/14 season Sean Thornton was released from Conwy for breaching Club rules.[citation needed]

On 4 January 2015 Sean agreed to sign for hometown club Drogheda United in what would be his first experience of playing in the League of Ireland. Thornton signed along with former Athlone Town player Sean Brennan. [46]

^"Doncaster 3–0 Aston Villa". BBC Sport. 29 November 2005. Retrieved 2009-06-19. Thornton was another prodigious influence for Doncaster in midfield and he capped a fine performance by scoring their third goal.

^Pearson, James (29 November 2005). "Sorry Villa crash to Rovers". Sky Sports. Retrieved 2009-06-19. Villa tried to get back into the contest, but their hopes were extinguished when the impressive Thornton bagged his first for the club. The blonde-haired maestro burst past a couple of defenders before seeing his drilled effort glance off the disappointing Ridgewell and into the net to book their place in the quarter finals.

^"Doncaster boss releases quintet". BBC Sport. 10 May 2007. Retrieved 2009-06-20. Doncaster have released Liam Green, Adam Brown, Rob Pacey, Jan Budtz and Sean Thornton. Midfielders Green, Brown, Thornton will all have to look for new clubs for the start of the season.